Starting phenix.real_space_refine on Thu Apr 11 15:22:56 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r1w_14242/04_2024/7r1w_14242.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r1w_14242/04_2024/7r1w_14242.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r1w_14242/04_2024/7r1w_14242.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r1w_14242/04_2024/7r1w_14242.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r1w_14242/04_2024/7r1w_14242.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r1w_14242/04_2024/7r1w_14242.pdb" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.010 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 32 5.16 5 C 7447 2.51 5 N 2022 2.21 5 O 2322 1.98 5 H 11363 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 76": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A GLU 90": "OE1" <-> "OE2" Residue "A GLU 115": "OE1" <-> "OE2" Residue "A GLU 176": "OE1" <-> "OE2" Residue "A GLU 192": "OE1" <-> "OE2" Residue "A GLU 224": "OE1" <-> "OE2" Residue "A ARG 321": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A GLU 368": "OE1" <-> "OE2" Residue "A ARG 391": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 404": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 421": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 526": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A GLU 607": "OE1" <-> "OE2" Residue "A GLU 645": "OE1" <-> "OE2" Residue "A ARG 661": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 734": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A GLU 800": "OE1" <-> "OE2" Residue "B GLU 26": "OE1" <-> "OE2" Residue "B GLU 39": "OE1" <-> "OE2" Residue "B GLU 99": "OE1" <-> "OE2" Residue "B GLU 150": "OE1" <-> "OE2" Residue "B ARG 215": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 273": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 281": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 304": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B GLU 343": "OE1" <-> "OE2" Residue "B ARG 355": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D GLU 187": "OE1" <-> "OE2" Residue "D ARG 203": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 78": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E GLU 84": "OE1" <-> "OE2" Residue "G TYR 8": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 23186 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 12122 Number of conformers: 1 Conformer: "" Number of residues, atoms: 786, 12122 Classifications: {'peptide': 786} Link IDs: {'PTRANS': 29, 'TRANS': 756} Chain: "B" Number of atoms: 5416 Number of conformers: 1 Conformer: "" Number of residues, atoms: 362, 5416 Classifications: {'peptide': 362} Link IDs: {'PTRANS': 11, 'TRANS': 350} Chain breaks: 1 Chain: "C" Number of atoms: 844 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 844 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 6, 'TRANS': 51} Chain: "D" Number of atoms: 3346 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 3346 Classifications: {'peptide': 209} Link IDs: {'PTRANS': 12, 'TRANS': 196} Chain breaks: 1 Chain: "E" Number of atoms: 1291 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 1291 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 5, 'TRANS': 78} Chain: "G" Number of atoms: 167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 167 Classifications: {'peptide': 10} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'TRANS': 9} Time building chain proxies: 10.51, per 1000 atoms: 0.45 Number of scatterers: 23186 At special positions: 0 Unit cell: (101.68, 134.48, 125.46, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 32 16.00 O 2322 8.00 N 2022 7.00 C 7447 6.00 H 11363 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 690 " - pdb=" SG CYS A 700 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 17.43 Conformation dependent library (CDL) restraints added in 2.7 seconds 2986 Ramachandran restraints generated. 1493 Oldfield, 0 Emsley, 1493 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2762 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 17 sheets defined 23.2% alpha, 30.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.52 Creating SS restraints... Processing helix chain 'A' and resid 38 through 46 Processing helix chain 'A' and resid 55 through 69 Processing helix chain 'A' and resid 106 through 118 Processing helix chain 'A' and resid 129 through 145 Processing helix chain 'A' and resid 189 through 195 Processing helix chain 'A' and resid 215 through 232 Processing helix chain 'A' and resid 280 through 286 removed outlier: 3.676A pdb=" N ILE A 284 " --> pdb=" O HIS A 280 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N GLU A 285 " --> pdb=" O SER A 281 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N GLN A 286 " --> pdb=" O ALA A 282 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 280 through 286' Processing helix chain 'A' and resid 297 through 315 removed outlier: 3.727A pdb=" N VAL A 301 " --> pdb=" O ASN A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 361 through 367 removed outlier: 3.714A pdb=" N LEU A 365 " --> pdb=" O LYS A 361 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 393 removed outlier: 3.660A pdb=" N LEU A 392 " --> pdb=" O ARG A 388 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N GLY A 393 " --> pdb=" O LEU A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 497 through 500 removed outlier: 3.952A pdb=" N ASP A 500 " --> pdb=" O ASP A 497 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 497 through 500' Processing helix chain 'A' and resid 542 through 550 removed outlier: 4.361A pdb=" N TYR A 548 " --> pdb=" O ALA A 544 " (cutoff:3.500A) Processing helix chain 'A' and resid 551 through 553 No H-bonds generated for 'chain 'A' and resid 551 through 553' Processing helix chain 'A' and resid 691 through 695 removed outlier: 3.573A pdb=" N GLY A 695 " --> pdb=" O THR A 692 " (cutoff:3.500A) Processing helix chain 'A' and resid 729 through 733 removed outlier: 3.617A pdb=" N VAL A 733 " --> pdb=" O ALA A 730 " (cutoff:3.500A) Processing helix chain 'C' and resid 30 through 33 Processing helix chain 'C' and resid 34 through 39 removed outlier: 3.997A pdb=" N ASP C 38 " --> pdb=" O GLN C 34 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLU C 39 " --> pdb=" O VAL C 35 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 34 through 39' Processing helix chain 'D' and resid 31 through 44 removed outlier: 3.541A pdb=" N ILE D 35 " --> pdb=" O PRO D 31 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLN D 44 " --> pdb=" O GLN D 40 " (cutoff:3.500A) Processing helix chain 'D' and resid 47 through 62 removed outlier: 4.215A pdb=" N ALA D 51 " --> pdb=" O ASN D 47 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N THR D 53 " --> pdb=" O ARG D 49 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLN D 54 " --> pdb=" O GLN D 50 " (cutoff:3.500A) Processing helix chain 'D' and resid 67 through 82 Processing helix chain 'D' and resid 84 through 99 Processing helix chain 'D' and resid 102 through 104 No H-bonds generated for 'chain 'D' and resid 102 through 104' Processing helix chain 'D' and resid 105 through 121 Processing helix chain 'D' and resid 137 through 154 Processing helix chain 'D' and resid 160 through 189 removed outlier: 3.785A pdb=" N PHE D 169 " --> pdb=" O LYS D 165 " (cutoff:3.500A) Processing helix chain 'D' and resid 191 through 205 removed outlier: 3.987A pdb=" N VAL D 195 " --> pdb=" O TRP D 191 " (cutoff:3.500A) Processing helix chain 'D' and resid 208 through 213 removed outlier: 3.964A pdb=" N ARG D 212 " --> pdb=" O THR D 208 " (cutoff:3.500A) Processing helix chain 'D' and resid 214 through 225 Processing helix chain 'D' and resid 227 through 240 removed outlier: 3.955A pdb=" N LYS D 233 " --> pdb=" O ALA D 229 " (cutoff:3.500A) Processing helix chain 'E' and resid 51 through 59 Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 32 removed outlier: 3.773A pdb=" N HIS A 30 " --> pdb=" O LEU A 84 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N VAL A 86 " --> pdb=" O HIS A 30 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ASP A 74 " --> pdb=" O LYS A 89 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 93 through 100 removed outlier: 7.501A pdb=" N LEU A 165 " --> pdb=" O ALA A 95 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N ILE A 97 " --> pdb=" O LEU A 165 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N LEU A 167 " --> pdb=" O ILE A 97 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N PHE A 99 " --> pdb=" O LEU A 167 " (cutoff:3.500A) removed outlier: 7.478A pdb=" N PHE A 169 " --> pdb=" O PHE A 99 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 176 through 183 removed outlier: 7.638A pdb=" N VAL A 256 " --> pdb=" O GLN A 178 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N ILE A 180 " --> pdb=" O VAL A 256 " (cutoff:3.500A) removed outlier: 7.494A pdb=" N VAL A 258 " --> pdb=" O ILE A 180 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N ILE A 182 " --> pdb=" O VAL A 258 " (cutoff:3.500A) removed outlier: 7.249A pdb=" N ILE A 260 " --> pdb=" O ILE A 182 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N SER A 242 " --> pdb=" O ASN A 259 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N THR A 261 " --> pdb=" O ILE A 240 " (cutoff:3.500A) removed outlier: 5.991A pdb=" N ILE A 240 " --> pdb=" O THR A 261 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 294 through 295 removed outlier: 3.859A pdb=" N GLU A 294 " --> pdb=" O LEU A 268 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N LYS A 267 " --> pdb=" O VAL A 335 " (cutoff:3.500A) removed outlier: 7.436A pdb=" N LEU A 337 " --> pdb=" O LYS A 267 " (cutoff:3.500A) removed outlier: 8.489A pdb=" N SER A 269 " --> pdb=" O LEU A 337 " (cutoff:3.500A) removed outlier: 12.767A pdb=" N VAL A 339 " --> pdb=" O SER A 269 " (cutoff:3.500A) removed outlier: 9.912A pdb=" N VAL A 271 " --> pdb=" O VAL A 339 " (cutoff:3.500A) removed outlier: 12.237A pdb=" N VAL A 341 " --> pdb=" O VAL A 271 " (cutoff:3.500A) removed outlier: 9.827A pdb=" N VAL A 273 " --> pdb=" O VAL A 341 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 348 through 355 removed outlier: 7.531A pdb=" N VAL A 414 " --> pdb=" O ARG A 350 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N ILE A 352 " --> pdb=" O VAL A 414 " (cutoff:3.500A) removed outlier: 7.160A pdb=" N TYR A 416 " --> pdb=" O ILE A 352 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N PHE A 354 " --> pdb=" O TYR A 416 " (cutoff:3.500A) removed outlier: 7.308A pdb=" N VAL A 418 " --> pdb=" O PHE A 354 " (cutoff:3.500A) removed outlier: 7.897A pdb=" N GLN A 411 " --> pdb=" O ARG A 404 " (cutoff:3.500A) removed outlier: 5.396A pdb=" N ARG A 404 " --> pdb=" O GLN A 411 " (cutoff:3.500A) removed outlier: 5.797A pdb=" N ASP A 413 " --> pdb=" O THR A 402 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N THR A 402 " --> pdb=" O ASP A 413 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N VAL A 415 " --> pdb=" O THR A 400 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N THR A 400 " --> pdb=" O VAL A 415 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N LYS A 417 " --> pdb=" O VAL A 398 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N VAL A 398 " --> pdb=" O LYS A 417 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N LYS A 419 " --> pdb=" O GLU A 396 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 426 through 433 removed outlier: 3.766A pdb=" N GLN A 466 " --> pdb=" O ASN A 463 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 426 through 433 removed outlier: 3.766A pdb=" N GLN A 466 " --> pdb=" O ASN A 463 " (cutoff:3.500A) removed outlier: 5.224A pdb=" N TYR A 608 " --> pdb=" O THR A 600 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N THR A 735 " --> pdb=" O THR A 720 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 662 through 663 removed outlier: 3.973A pdb=" N GLY A 662 " --> pdb=" O GLU A 800 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 48 through 50 removed outlier: 3.673A pdb=" N TRP B 48 " --> pdb=" O SER B 389 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N LEU B 378 " --> pdb=" O ILE B 390 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 71 through 75 removed outlier: 3.996A pdb=" N TRP B 93 " --> pdb=" O ALA B 83 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ASN B 85 " --> pdb=" O GLU B 91 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N GLU B 91 " --> pdb=" O ASN B 85 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 116 through 117 removed outlier: 6.307A pdb=" N ASN B 135 " --> pdb=" O VAL B 141 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N VAL B 141 " --> pdb=" O ASN B 135 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 156 through 158 removed outlier: 3.784A pdb=" N TRP B 183 " --> pdb=" O ALA B 173 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 201 through 203 removed outlier: 3.870A pdb=" N TRP B 228 " --> pdb=" O ALA B 218 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N LEU B 220 " --> pdb=" O MET B 226 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N MET B 226 " --> pdb=" O LEU B 220 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 252 through 254 removed outlier: 6.505A pdb=" N LEU B 267 " --> pdb=" O LYS B 280 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N LYS B 280 " --> pdb=" O LEU B 267 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N ALA B 269 " --> pdb=" O MET B 278 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 290 through 292 removed outlier: 6.949A pdb=" N VAL B 305 " --> pdb=" O THR B 318 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N THR B 318 " --> pdb=" O VAL B 305 " (cutoff:3.500A) removed outlier: 7.117A pdb=" N ALA B 307 " --> pdb=" O LEU B 316 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 331 through 333 Processing sheet with id=AB8, first strand: chain 'E' and resid 32 through 35 531 hydrogen bonds defined for protein. 1479 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 8.62 Time building geometry restraints manager: 18.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 11312 1.03 - 1.23: 66 1.23 - 1.42: 5227 1.42 - 1.62: 6778 1.62 - 1.82: 62 Bond restraints: 23445 Sorted by residual: bond pdb=" CA ASN G 2 " pdb=" C ASN G 2 " ideal model delta sigma weight residual 1.533 1.398 0.135 9.60e-03 1.09e+04 1.99e+02 bond pdb=" C SER G 3 " pdb=" O SER G 3 " ideal model delta sigma weight residual 1.235 1.372 -0.137 1.26e-02 6.30e+03 1.18e+02 bond pdb=" CA HIS G 6 " pdb=" C HIS G 6 " ideal model delta sigma weight residual 1.523 1.388 0.135 1.34e-02 5.57e+03 1.02e+02 bond pdb=" CA SER G 7 " pdb=" C SER G 7 " ideal model delta sigma weight residual 1.525 1.398 0.127 1.29e-02 6.01e+03 9.75e+01 bond pdb=" CA SER G 3 " pdb=" C SER G 3 " ideal model delta sigma weight residual 1.523 1.401 0.122 1.34e-02 5.57e+03 8.27e+01 ... (remaining 23440 not shown) Histogram of bond angle deviations from ideal: 89.65 - 98.53: 2 98.53 - 107.41: 820 107.41 - 116.29: 28835 116.29 - 125.17: 12075 125.17 - 134.05: 415 Bond angle restraints: 42147 Sorted by residual: angle pdb=" N TYR G 8 " pdb=" CA TYR G 8 " pdb=" C TYR G 8 " ideal model delta sigma weight residual 109.71 123.48 -13.77 1.41e+00 5.03e-01 9.53e+01 angle pdb=" N SER G 7 " pdb=" CA SER G 7 " pdb=" C SER G 7 " ideal model delta sigma weight residual 107.75 89.65 18.10 1.86e+00 2.89e-01 9.46e+01 angle pdb=" CA SER G 7 " pdb=" C SER G 7 " pdb=" N TYR G 8 " ideal model delta sigma weight residual 116.21 127.68 -11.47 1.36e+00 5.41e-01 7.11e+01 angle pdb=" CA HIS G 6 " pdb=" CB HIS G 6 " pdb=" CG HIS G 6 " ideal model delta sigma weight residual 113.80 121.14 -7.34 1.00e+00 1.00e+00 5.38e+01 angle pdb=" O SER G 7 " pdb=" C SER G 7 " pdb=" N TYR G 8 " ideal model delta sigma weight residual 122.87 113.93 8.94 1.23e+00 6.61e-01 5.28e+01 ... (remaining 42142 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.55: 10043 17.55 - 35.10: 794 35.10 - 52.66: 224 52.66 - 70.21: 49 70.21 - 87.76: 13 Dihedral angle restraints: 11123 sinusoidal: 5982 harmonic: 5141 Sorted by residual: dihedral pdb=" CA LEU A 699 " pdb=" C LEU A 699 " pdb=" N CYS A 700 " pdb=" CA CYS A 700 " ideal model delta harmonic sigma weight residual -180.00 -157.56 -22.44 0 5.00e+00 4.00e-02 2.01e+01 dihedral pdb=" CA GLU C 39 " pdb=" C GLU C 39 " pdb=" N ALA C 40 " pdb=" CA ALA C 40 " ideal model delta harmonic sigma weight residual 180.00 -159.68 -20.32 0 5.00e+00 4.00e-02 1.65e+01 dihedral pdb=" C SER G 7 " pdb=" N SER G 7 " pdb=" CA SER G 7 " pdb=" CB SER G 7 " ideal model delta harmonic sigma weight residual -122.60 -113.64 -8.96 0 2.50e+00 1.60e-01 1.28e+01 ... (remaining 11120 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 1590 0.070 - 0.140: 181 0.140 - 0.210: 9 0.210 - 0.280: 3 0.280 - 0.350: 2 Chirality restraints: 1785 Sorted by residual: chirality pdb=" CA TRP G 1 " pdb=" N TRP G 1 " pdb=" C TRP G 1 " pdb=" CB TRP G 1 " both_signs ideal model delta sigma weight residual False 2.57 2.22 0.35 2.00e-01 2.50e+01 3.07e+00 chirality pdb=" CA VAL G 5 " pdb=" N VAL G 5 " pdb=" C VAL G 5 " pdb=" CB VAL G 5 " both_signs ideal model delta sigma weight residual False 2.44 2.73 -0.29 2.00e-01 2.50e+01 2.09e+00 chirality pdb=" CA ASN G 4 " pdb=" N ASN G 4 " pdb=" C ASN G 4 " pdb=" CB ASN G 4 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.47e+00 ... (remaining 1782 not shown) Planarity restraints: 3595 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 427 " 0.113 2.00e-02 2.50e+03 1.19e-01 2.13e+02 pdb=" CG ASN A 427 " -0.009 2.00e-02 2.50e+03 pdb=" OD1 ASN A 427 " -0.107 2.00e-02 2.50e+03 pdb=" ND2 ASN A 427 " -0.002 2.00e-02 2.50e+03 pdb="HD21 ASN A 427 " 0.177 2.00e-02 2.50e+03 pdb="HD22 ASN A 427 " -0.172 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS G 6 " 0.063 2.00e-02 2.50e+03 5.31e-02 5.63e+01 pdb=" CG HIS G 6 " -0.112 2.00e-02 2.50e+03 pdb=" ND1 HIS G 6 " -0.026 2.00e-02 2.50e+03 pdb=" CD2 HIS G 6 " 0.050 2.00e-02 2.50e+03 pdb=" CE1 HIS G 6 " 0.035 2.00e-02 2.50e+03 pdb=" NE2 HIS G 6 " -0.032 2.00e-02 2.50e+03 pdb=" HD2 HIS G 6 " -0.003 2.00e-02 2.50e+03 pdb=" HE1 HIS G 6 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 186 " -0.020 2.00e-02 2.50e+03 2.99e-02 1.34e+01 pdb=" CG ASN B 186 " 0.064 2.00e-02 2.50e+03 pdb=" OD1 ASN B 186 " -0.026 2.00e-02 2.50e+03 pdb=" ND2 ASN B 186 " -0.001 2.00e-02 2.50e+03 pdb="HD21 ASN B 186 " -0.008 2.00e-02 2.50e+03 pdb="HD22 ASN B 186 " -0.009 2.00e-02 2.50e+03 ... (remaining 3592 not shown) Histogram of nonbonded interaction distances: 1.39 - 2.03: 263 2.03 - 2.67: 33712 2.67 - 3.31: 62877 3.31 - 3.96: 82604 3.96 - 4.60: 130185 Nonbonded interactions: 309641 Sorted by model distance: nonbonded pdb=" CH2 TRP G 1 " pdb=" CB ASN G 4 " model vdw 1.387 3.450 nonbonded pdb=" NE2 HIS G 6 " pdb=" CB TYR G 8 " model vdw 1.482 3.250 nonbonded pdb=" HG SER A 502 " pdb=" OE1 GLN A 542 " model vdw 1.531 1.850 nonbonded pdb=" HH TYR A 674 " pdb=" OD2 ASP A 704 " model vdw 1.557 1.850 nonbonded pdb=" H LYS A 103 " pdb=" OE2 GLU A 171 " model vdw 1.561 1.850 ... (remaining 309636 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.980 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.360 Extract box with map and model: 10.760 Check model and map are aligned: 0.350 Set scattering table: 0.210 Process input model: 72.460 Find NCS groups from input model: 0.590 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 90.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.138 12082 Z= 0.353 Angle : 0.686 18.096 16420 Z= 0.415 Chirality : 0.046 0.350 1785 Planarity : 0.004 0.059 2163 Dihedral : 13.744 87.759 4374 Min Nonbonded Distance : 1.387 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.27 % Allowed : 4.69 % Favored : 95.04 % Rotamer: Outliers : 0.16 % Allowed : 0.24 % Favored : 99.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.64 (0.20), residues: 1493 helix: 0.02 (0.29), residues: 312 sheet: -1.60 (0.21), residues: 460 loop : -2.70 (0.20), residues: 721 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP G 1 HIS 0.069 0.003 HIS G 6 PHE 0.017 0.001 PHE E 74 TYR 0.021 0.001 TYR A 142 ARG 0.039 0.001 ARG D 97 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2986 Ramachandran restraints generated. 1493 Oldfield, 0 Emsley, 1493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2986 Ramachandran restraints generated. 1493 Oldfield, 0 Emsley, 1493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 1267 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 107 time to evaluate : 1.905 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 325 MET cc_start: 0.6859 (tmm) cc_final: 0.6575 (tmm) REVERT: C 81 ASP cc_start: 0.8173 (t0) cc_final: 0.7678 (t0) REVERT: D 34 GLU cc_start: 0.8988 (mp0) cc_final: 0.8717 (mp0) REVERT: E 50 MET cc_start: 0.8133 (mtp) cc_final: 0.7927 (mtp) outliers start: 2 outliers final: 1 residues processed: 109 average time/residue: 0.5465 time to fit residues: 88.5280 Evaluate side-chains 80 residues out of total 1267 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 79 time to evaluate : 1.857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 10 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 124 optimal weight: 3.9990 chunk 112 optimal weight: 0.6980 chunk 62 optimal weight: 0.0470 chunk 38 optimal weight: 0.5980 chunk 75 optimal weight: 0.9980 chunk 59 optimal weight: 2.9990 chunk 116 optimal weight: 0.6980 chunk 44 optimal weight: 1.9990 chunk 70 optimal weight: 0.0980 chunk 86 optimal weight: 0.6980 chunk 134 optimal weight: 2.9990 overall best weight: 0.4278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 259 ASN B 168 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.0874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 12082 Z= 0.146 Angle : 0.496 7.154 16420 Z= 0.266 Chirality : 0.043 0.151 1785 Planarity : 0.004 0.058 2163 Dihedral : 4.454 53.353 1657 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.62 % Favored : 96.32 % Rotamer: Outliers : 0.47 % Allowed : 4.50 % Favored : 95.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.01 (0.20), residues: 1493 helix: 0.59 (0.29), residues: 329 sheet: -1.08 (0.22), residues: 447 loop : -2.48 (0.20), residues: 717 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 348 HIS 0.002 0.001 HIS A 677 PHE 0.009 0.001 PHE A 426 TYR 0.014 0.001 TYR D 184 ARG 0.006 0.000 ARG D 97 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2986 Ramachandran restraints generated. 1493 Oldfield, 0 Emsley, 1493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2986 Ramachandran restraints generated. 1493 Oldfield, 0 Emsley, 1493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 1267 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 94 time to evaluate : 1.746 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 325 MET cc_start: 0.6940 (tmm) cc_final: 0.6668 (tmm) REVERT: A 401 ASP cc_start: 0.7870 (t0) cc_final: 0.7620 (t0) REVERT: C 81 ASP cc_start: 0.8164 (t0) cc_final: 0.7662 (t0) REVERT: D 148 SER cc_start: 0.8822 (m) cc_final: 0.8596 (p) REVERT: E 46 ILE cc_start: 0.8917 (OUTLIER) cc_final: 0.8570 (pp) REVERT: E 47 ARG cc_start: 0.8449 (mmm160) cc_final: 0.8171 (mmp-170) REVERT: E 50 MET cc_start: 0.8161 (mtp) cc_final: 0.7933 (mtp) outliers start: 6 outliers final: 5 residues processed: 97 average time/residue: 0.5090 time to fit residues: 73.0531 Evaluate side-chains 90 residues out of total 1267 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 84 time to evaluate : 1.905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 470 GLU Chi-restraints excluded: chain A residue 741 MET Chi-restraints excluded: chain A residue 746 ASP Chi-restraints excluded: chain D residue 237 ILE Chi-restraints excluded: chain E residue 46 ILE Chi-restraints excluded: chain G residue 10 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 74 optimal weight: 1.9990 chunk 41 optimal weight: 3.9990 chunk 111 optimal weight: 3.9990 chunk 91 optimal weight: 0.2980 chunk 37 optimal weight: 3.9990 chunk 134 optimal weight: 2.9990 chunk 145 optimal weight: 2.9990 chunk 119 optimal weight: 1.9990 chunk 133 optimal weight: 0.9990 chunk 45 optimal weight: 2.9990 chunk 108 optimal weight: 3.9990 overall best weight: 1.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 561 GLN D 82 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.1780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.084 12082 Z= 0.257 Angle : 0.511 5.601 16420 Z= 0.276 Chirality : 0.043 0.150 1785 Planarity : 0.004 0.045 2163 Dihedral : 4.269 36.302 1657 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.89 % Favored : 95.04 % Rotamer: Outliers : 0.95 % Allowed : 5.68 % Favored : 93.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.49 (0.20), residues: 1493 helix: 1.17 (0.29), residues: 323 sheet: -0.91 (0.23), residues: 464 loop : -2.11 (0.21), residues: 706 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 776 HIS 0.004 0.001 HIS D 139 PHE 0.009 0.001 PHE E 74 TYR 0.014 0.001 TYR D 184 ARG 0.004 0.000 ARG G 9 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2986 Ramachandran restraints generated. 1493 Oldfield, 0 Emsley, 1493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2986 Ramachandran restraints generated. 1493 Oldfield, 0 Emsley, 1493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 1267 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 91 time to evaluate : 1.873 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 109 MET cc_start: 0.8078 (tmm) cc_final: 0.7732 (tmm) REVERT: A 325 MET cc_start: 0.7170 (tmm) cc_final: 0.6833 (tmm) REVERT: A 401 ASP cc_start: 0.7974 (t0) cc_final: 0.7735 (t0) REVERT: C 81 ASP cc_start: 0.8204 (t0) cc_final: 0.7803 (t0) REVERT: E 97 SER cc_start: 0.9172 (m) cc_final: 0.8889 (t) outliers start: 12 outliers final: 9 residues processed: 98 average time/residue: 0.4933 time to fit residues: 74.3552 Evaluate side-chains 86 residues out of total 1267 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 77 time to evaluate : 1.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 470 GLU Chi-restraints excluded: chain A residue 573 ASN Chi-restraints excluded: chain A residue 741 MET Chi-restraints excluded: chain B residue 248 ASP Chi-restraints excluded: chain D residue 56 GLU Chi-restraints excluded: chain D residue 64 PHE Chi-restraints excluded: chain D residue 186 THR Chi-restraints excluded: chain D residue 237 ILE Chi-restraints excluded: chain G residue 10 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 133 optimal weight: 1.9990 chunk 101 optimal weight: 5.9990 chunk 69 optimal weight: 3.9990 chunk 14 optimal weight: 6.9990 chunk 64 optimal weight: 1.9990 chunk 90 optimal weight: 3.9990 chunk 135 optimal weight: 0.5980 chunk 143 optimal weight: 0.5980 chunk 70 optimal weight: 0.0070 chunk 128 optimal weight: 3.9990 chunk 38 optimal weight: 0.5980 overall best weight: 0.7600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 368 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.1997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 12082 Z= 0.137 Angle : 0.452 4.373 16420 Z= 0.241 Chirality : 0.042 0.145 1785 Planarity : 0.003 0.050 2163 Dihedral : 4.063 31.627 1657 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.75 % Favored : 97.19 % Rotamer: Outliers : 0.71 % Allowed : 7.26 % Favored : 92.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.09 (0.21), residues: 1493 helix: 1.48 (0.29), residues: 329 sheet: -0.61 (0.23), residues: 464 loop : -1.92 (0.21), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 348 HIS 0.002 0.001 HIS A 280 PHE 0.014 0.001 PHE A 197 TYR 0.014 0.001 TYR D 184 ARG 0.004 0.000 ARG G 9 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2986 Ramachandran restraints generated. 1493 Oldfield, 0 Emsley, 1493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2986 Ramachandran restraints generated. 1493 Oldfield, 0 Emsley, 1493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 1267 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 89 time to evaluate : 1.892 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 109 MET cc_start: 0.8078 (tmm) cc_final: 0.7717 (tmm) REVERT: A 325 MET cc_start: 0.7151 (tmm) cc_final: 0.6877 (tmm) REVERT: A 394 PHE cc_start: 0.8580 (m-10) cc_final: 0.8284 (m-10) REVERT: A 401 ASP cc_start: 0.7945 (t0) cc_final: 0.7693 (t0) REVERT: C 81 ASP cc_start: 0.8175 (t0) cc_final: 0.7776 (t0) REVERT: E 97 SER cc_start: 0.9165 (m) cc_final: 0.8893 (t) outliers start: 9 outliers final: 7 residues processed: 96 average time/residue: 0.4838 time to fit residues: 69.5082 Evaluate side-chains 90 residues out of total 1267 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 83 time to evaluate : 1.921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 ASP Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 470 GLU Chi-restraints excluded: chain D residue 56 GLU Chi-restraints excluded: chain D residue 76 ILE Chi-restraints excluded: chain D residue 205 TYR Chi-restraints excluded: chain G residue 10 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 119 optimal weight: 1.9990 chunk 81 optimal weight: 3.9990 chunk 2 optimal weight: 20.0000 chunk 106 optimal weight: 0.5980 chunk 59 optimal weight: 0.0870 chunk 122 optimal weight: 3.9990 chunk 98 optimal weight: 4.9990 chunk 0 optimal weight: 30.0000 chunk 73 optimal weight: 0.9990 chunk 128 optimal weight: 4.9990 chunk 36 optimal weight: 2.9990 overall best weight: 1.3364 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 748 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 102 HIS G 2 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.2422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 12082 Z= 0.208 Angle : 0.467 4.299 16420 Z= 0.249 Chirality : 0.042 0.143 1785 Planarity : 0.003 0.050 2163 Dihedral : 3.996 28.214 1657 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.95 % Favored : 95.98 % Rotamer: Outliers : 1.10 % Allowed : 7.02 % Favored : 91.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.90 (0.21), residues: 1493 helix: 1.61 (0.29), residues: 330 sheet: -0.52 (0.23), residues: 455 loop : -1.74 (0.22), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 348 HIS 0.003 0.001 HIS D 139 PHE 0.009 0.001 PHE A 140 TYR 0.013 0.001 TYR D 184 ARG 0.005 0.000 ARG G 9 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2986 Ramachandran restraints generated. 1493 Oldfield, 0 Emsley, 1493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2986 Ramachandran restraints generated. 1493 Oldfield, 0 Emsley, 1493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 1267 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 85 time to evaluate : 1.818 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 109 MET cc_start: 0.8004 (tmm) cc_final: 0.7640 (tmm) REVERT: A 325 MET cc_start: 0.7223 (tmm) cc_final: 0.6947 (tmm) REVERT: A 394 PHE cc_start: 0.8611 (m-10) cc_final: 0.8272 (m-10) REVERT: A 401 ASP cc_start: 0.7970 (t0) cc_final: 0.7726 (t0) REVERT: C 81 ASP cc_start: 0.8198 (t0) cc_final: 0.7861 (t0) REVERT: D 183 GLU cc_start: 0.8602 (tp30) cc_final: 0.8261 (tp30) REVERT: E 97 SER cc_start: 0.9199 (m) cc_final: 0.8952 (t) outliers start: 14 outliers final: 13 residues processed: 96 average time/residue: 0.5100 time to fit residues: 73.2723 Evaluate side-chains 95 residues out of total 1267 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 82 time to evaluate : 1.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 ASP Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 461 THR Chi-restraints excluded: chain A residue 470 GLU Chi-restraints excluded: chain A residue 666 ASN Chi-restraints excluded: chain A residue 741 MET Chi-restraints excluded: chain B residue 248 ASP Chi-restraints excluded: chain D residue 56 GLU Chi-restraints excluded: chain D residue 76 ILE Chi-restraints excluded: chain D residue 186 THR Chi-restraints excluded: chain D residue 205 TYR Chi-restraints excluded: chain G residue 2 ASN Chi-restraints excluded: chain G residue 10 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 48 optimal weight: 2.9990 chunk 128 optimal weight: 3.9990 chunk 28 optimal weight: 3.9990 chunk 83 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 143 optimal weight: 2.9990 chunk 118 optimal weight: 6.9990 chunk 66 optimal weight: 0.2980 chunk 11 optimal weight: 5.9990 chunk 47 optimal weight: 0.9990 chunk 75 optimal weight: 0.6980 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 2 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.2604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 12082 Z= 0.203 Angle : 0.459 4.382 16420 Z= 0.245 Chirality : 0.042 0.141 1785 Planarity : 0.003 0.048 2163 Dihedral : 3.980 25.843 1657 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.55 % Favored : 96.38 % Rotamer: Outliers : 1.03 % Allowed : 7.89 % Favored : 91.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.70 (0.21), residues: 1493 helix: 1.91 (0.30), residues: 321 sheet: -0.44 (0.23), residues: 454 loop : -1.62 (0.22), residues: 718 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 393 HIS 0.002 0.001 HIS D 139 PHE 0.009 0.001 PHE A 140 TYR 0.014 0.001 TYR D 184 ARG 0.006 0.000 ARG G 9 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2986 Ramachandran restraints generated. 1493 Oldfield, 0 Emsley, 1493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2986 Ramachandran restraints generated. 1493 Oldfield, 0 Emsley, 1493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 1267 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 85 time to evaluate : 1.867 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 109 MET cc_start: 0.7979 (tmm) cc_final: 0.7597 (tmm) REVERT: A 325 MET cc_start: 0.7221 (tmm) cc_final: 0.6941 (tmm) REVERT: A 394 PHE cc_start: 0.8589 (m-10) cc_final: 0.8177 (m-10) REVERT: A 401 ASP cc_start: 0.7982 (t0) cc_final: 0.7734 (t0) REVERT: C 78 LYS cc_start: 0.8623 (mtmm) cc_final: 0.8353 (mtmm) REVERT: C 81 ASP cc_start: 0.8211 (t0) cc_final: 0.7888 (t0) REVERT: D 183 GLU cc_start: 0.8591 (tp30) cc_final: 0.8232 (tp30) REVERT: E 97 SER cc_start: 0.9181 (m) cc_final: 0.8954 (t) outliers start: 13 outliers final: 11 residues processed: 94 average time/residue: 0.4957 time to fit residues: 70.3639 Evaluate side-chains 90 residues out of total 1267 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 79 time to evaluate : 1.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 ASP Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 461 THR Chi-restraints excluded: chain A residue 470 GLU Chi-restraints excluded: chain A residue 573 ASN Chi-restraints excluded: chain A residue 741 MET Chi-restraints excluded: chain B residue 248 ASP Chi-restraints excluded: chain D residue 56 GLU Chi-restraints excluded: chain D residue 76 ILE Chi-restraints excluded: chain D residue 205 TYR Chi-restraints excluded: chain G residue 10 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 138 optimal weight: 3.9990 chunk 16 optimal weight: 3.9990 chunk 81 optimal weight: 2.9990 chunk 104 optimal weight: 3.9990 chunk 120 optimal weight: 6.9990 chunk 79 optimal weight: 3.9990 chunk 142 optimal weight: 1.9990 chunk 89 optimal weight: 1.9990 chunk 86 optimal weight: 0.9980 chunk 65 optimal weight: 0.9980 chunk 88 optimal weight: 1.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 748 ASN E 88 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.2948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 12082 Z= 0.232 Angle : 0.475 5.334 16420 Z= 0.254 Chirality : 0.042 0.140 1785 Planarity : 0.004 0.058 2163 Dihedral : 3.980 23.169 1657 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.95 % Favored : 95.98 % Rotamer: Outliers : 1.18 % Allowed : 8.21 % Favored : 90.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.21), residues: 1493 helix: 1.95 (0.29), residues: 321 sheet: -0.34 (0.23), residues: 458 loop : -1.55 (0.22), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 393 HIS 0.003 0.001 HIS B 165 PHE 0.010 0.001 PHE A 140 TYR 0.013 0.001 TYR D 184 ARG 0.009 0.000 ARG G 9 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2986 Ramachandran restraints generated. 1493 Oldfield, 0 Emsley, 1493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2986 Ramachandran restraints generated. 1493 Oldfield, 0 Emsley, 1493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 1267 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 81 time to evaluate : 2.064 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 109 MET cc_start: 0.7935 (tmm) cc_final: 0.7535 (tmm) REVERT: A 325 MET cc_start: 0.7284 (tmm) cc_final: 0.7005 (tmm) REVERT: A 401 ASP cc_start: 0.7975 (t0) cc_final: 0.7620 (t0) REVERT: C 41 TYR cc_start: 0.6431 (p90) cc_final: 0.6209 (p90) REVERT: C 78 LYS cc_start: 0.8471 (mtmm) cc_final: 0.7880 (mtmm) REVERT: C 81 ASP cc_start: 0.8240 (t0) cc_final: 0.7913 (t0) REVERT: D 183 GLU cc_start: 0.8573 (tp30) cc_final: 0.8258 (tp30) REVERT: E 97 SER cc_start: 0.9232 (m) cc_final: 0.9027 (t) outliers start: 15 outliers final: 13 residues processed: 93 average time/residue: 0.4945 time to fit residues: 69.2184 Evaluate side-chains 90 residues out of total 1267 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 77 time to evaluate : 1.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 ASP Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 461 THR Chi-restraints excluded: chain A residue 470 GLU Chi-restraints excluded: chain A residue 573 ASN Chi-restraints excluded: chain A residue 741 MET Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 248 ASP Chi-restraints excluded: chain D residue 56 GLU Chi-restraints excluded: chain D residue 76 ILE Chi-restraints excluded: chain D residue 186 THR Chi-restraints excluded: chain D residue 205 TYR Chi-restraints excluded: chain G residue 10 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 56 optimal weight: 0.9990 chunk 85 optimal weight: 3.9990 chunk 42 optimal weight: 0.0060 chunk 28 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 chunk 90 optimal weight: 0.9990 chunk 97 optimal weight: 4.9990 chunk 70 optimal weight: 0.0370 chunk 13 optimal weight: 0.0870 chunk 112 optimal weight: 0.0770 chunk 129 optimal weight: 3.9990 overall best weight: 0.2412 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.3043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 12082 Z= 0.113 Angle : 0.444 7.789 16420 Z= 0.233 Chirality : 0.042 0.139 1785 Planarity : 0.003 0.062 2163 Dihedral : 3.790 18.028 1657 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.75 % Favored : 97.19 % Rotamer: Outliers : 0.79 % Allowed : 9.00 % Favored : 90.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.22), residues: 1493 helix: 2.33 (0.30), residues: 321 sheet: -0.16 (0.23), residues: 456 loop : -1.41 (0.22), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 348 HIS 0.002 0.000 HIS A 280 PHE 0.009 0.001 PHE A 140 TYR 0.015 0.001 TYR D 184 ARG 0.007 0.000 ARG G 9 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2986 Ramachandran restraints generated. 1493 Oldfield, 0 Emsley, 1493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2986 Ramachandran restraints generated. 1493 Oldfield, 0 Emsley, 1493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 1267 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 85 time to evaluate : 1.972 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 109 MET cc_start: 0.7942 (tmm) cc_final: 0.7545 (tmm) REVERT: A 325 MET cc_start: 0.7207 (tmm) cc_final: 0.6965 (tmm) REVERT: A 401 ASP cc_start: 0.7957 (t0) cc_final: 0.7704 (t0) REVERT: B 380 ILE cc_start: 0.9211 (tt) cc_final: 0.8911 (tt) REVERT: C 81 ASP cc_start: 0.8222 (t0) cc_final: 0.7897 (t0) REVERT: E 97 SER cc_start: 0.9203 (m) cc_final: 0.8990 (t) outliers start: 10 outliers final: 10 residues processed: 92 average time/residue: 0.5049 time to fit residues: 68.7137 Evaluate side-chains 89 residues out of total 1267 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 79 time to evaluate : 1.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 ASP Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 470 GLU Chi-restraints excluded: chain A residue 573 ASN Chi-restraints excluded: chain A residue 741 MET Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain D residue 56 GLU Chi-restraints excluded: chain D residue 76 ILE Chi-restraints excluded: chain D residue 205 TYR Chi-restraints excluded: chain G residue 10 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 136 optimal weight: 3.9990 chunk 124 optimal weight: 2.9990 chunk 132 optimal weight: 1.9990 chunk 80 optimal weight: 2.9990 chunk 57 optimal weight: 1.9990 chunk 104 optimal weight: 3.9990 chunk 40 optimal weight: 0.4980 chunk 120 optimal weight: 6.9990 chunk 125 optimal weight: 0.8980 chunk 87 optimal weight: 3.9990 chunk 140 optimal weight: 0.7980 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.3207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 12082 Z= 0.194 Angle : 0.460 6.139 16420 Z= 0.244 Chirality : 0.041 0.137 1785 Planarity : 0.003 0.056 2163 Dihedral : 3.789 16.580 1657 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.42 % Favored : 96.52 % Rotamer: Outliers : 0.79 % Allowed : 9.23 % Favored : 89.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.22), residues: 1493 helix: 2.33 (0.29), residues: 321 sheet: -0.14 (0.24), residues: 453 loop : -1.35 (0.22), residues: 719 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 393 HIS 0.003 0.001 HIS B 165 PHE 0.010 0.001 PHE A 197 TYR 0.014 0.001 TYR D 184 ARG 0.009 0.000 ARG G 9 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2986 Ramachandran restraints generated. 1493 Oldfield, 0 Emsley, 1493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2986 Ramachandran restraints generated. 1493 Oldfield, 0 Emsley, 1493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 1267 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 83 time to evaluate : 1.855 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 109 MET cc_start: 0.7965 (tmm) cc_final: 0.7562 (tmm) REVERT: A 325 MET cc_start: 0.7255 (tmm) cc_final: 0.6985 (tmm) REVERT: A 401 ASP cc_start: 0.7921 (t0) cc_final: 0.7676 (t0) REVERT: B 380 ILE cc_start: 0.9214 (tt) cc_final: 0.8913 (tt) REVERT: C 81 ASP cc_start: 0.8213 (t0) cc_final: 0.7032 (p0) REVERT: D 183 GLU cc_start: 0.8568 (tp30) cc_final: 0.8199 (tp30) outliers start: 10 outliers final: 10 residues processed: 90 average time/residue: 0.5242 time to fit residues: 69.5317 Evaluate side-chains 89 residues out of total 1267 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 79 time to evaluate : 1.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 ASP Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 470 GLU Chi-restraints excluded: chain A residue 573 ASN Chi-restraints excluded: chain A residue 741 MET Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain D residue 56 GLU Chi-restraints excluded: chain D residue 76 ILE Chi-restraints excluded: chain D residue 205 TYR Chi-restraints excluded: chain G residue 10 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 85 optimal weight: 4.9990 chunk 66 optimal weight: 0.0980 chunk 97 optimal weight: 5.9990 chunk 147 optimal weight: 0.9980 chunk 135 optimal weight: 1.9990 chunk 117 optimal weight: 1.9990 chunk 12 optimal weight: 7.9990 chunk 90 optimal weight: 2.9990 chunk 71 optimal weight: 2.9990 chunk 93 optimal weight: 0.8980 chunk 125 optimal weight: 0.8980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 158 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.3347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 12082 Z= 0.155 Angle : 0.450 6.492 16420 Z= 0.238 Chirality : 0.042 0.138 1785 Planarity : 0.003 0.063 2163 Dihedral : 3.733 17.460 1657 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 0.79 % Allowed : 9.23 % Favored : 89.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.22), residues: 1493 helix: 2.47 (0.29), residues: 321 sheet: -0.10 (0.23), residues: 459 loop : -1.27 (0.22), residues: 713 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 393 HIS 0.002 0.001 HIS B 165 PHE 0.009 0.001 PHE A 140 TYR 0.013 0.001 TYR D 184 ARG 0.009 0.000 ARG G 9 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2986 Ramachandran restraints generated. 1493 Oldfield, 0 Emsley, 1493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2986 Ramachandran restraints generated. 1493 Oldfield, 0 Emsley, 1493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 1267 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 83 time to evaluate : 1.804 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 109 MET cc_start: 0.7924 (tmm) cc_final: 0.7525 (tmm) REVERT: A 325 MET cc_start: 0.7232 (tmm) cc_final: 0.6961 (tmm) REVERT: A 401 ASP cc_start: 0.7938 (t0) cc_final: 0.7573 (t0) REVERT: B 380 ILE cc_start: 0.9202 (tt) cc_final: 0.8894 (tt) REVERT: C 81 ASP cc_start: 0.8237 (t0) cc_final: 0.7080 (p0) outliers start: 10 outliers final: 10 residues processed: 90 average time/residue: 0.5318 time to fit residues: 70.9649 Evaluate side-chains 90 residues out of total 1267 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 80 time to evaluate : 1.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 ASP Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 470 GLU Chi-restraints excluded: chain A residue 573 ASN Chi-restraints excluded: chain A residue 741 MET Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain D residue 56 GLU Chi-restraints excluded: chain D residue 76 ILE Chi-restraints excluded: chain D residue 205 TYR Chi-restraints excluded: chain G residue 10 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 35 optimal weight: 3.9990 chunk 108 optimal weight: 0.7980 chunk 17 optimal weight: 3.9990 chunk 32 optimal weight: 0.4980 chunk 117 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 120 optimal weight: 6.9990 chunk 14 optimal weight: 6.9990 chunk 21 optimal weight: 3.9990 chunk 103 optimal weight: 1.9990 chunk 6 optimal weight: 7.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.102667 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.075253 restraints weight = 79544.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.078763 restraints weight = 27430.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.080948 restraints weight = 15118.383| |-----------------------------------------------------------------------------| r_work (final): 0.3344 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.3504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 12082 Z= 0.220 Angle : 0.469 6.260 16420 Z= 0.249 Chirality : 0.042 0.180 1785 Planarity : 0.003 0.056 2163 Dihedral : 3.766 16.731 1657 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 0.71 % Allowed : 9.55 % Favored : 89.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.22), residues: 1493 helix: 2.47 (0.29), residues: 321 sheet: -0.07 (0.23), residues: 463 loop : -1.24 (0.23), residues: 709 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 393 HIS 0.003 0.001 HIS B 165 PHE 0.025 0.001 PHE A 197 TYR 0.013 0.001 TYR D 184 ARG 0.009 0.000 ARG G 9 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4402.62 seconds wall clock time: 79 minutes 30.77 seconds (4770.77 seconds total)